# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:33:06 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc3[nH]c(nc3c2)C4=C(N)c5c(F)cccc5NC4=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 38O  38O  4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one  ligand  50  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_38O
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 38O  C1   C  CH3   0  -0.518   8.6364   1.7135   0.1286
 38O  C3   C  CH2   0  -0.278   7.1686  -0.0502  -0.5571
 38O  C4   C  CH2   0  -0.312   5.9170  -0.8343  -0.2089
 38O  C6   C  CH2   0  -0.304   5.0104   1.1371   0.8176
 38O  C7   C  CH2   0  -0.282   6.2716   1.8931   0.4512
 38O  C8   C  CR6   0   0.357   3.4967  -0.5443  -0.0726
 38O  C12  C  CR5   0   0.585  -1.0059  -0.7521  -0.0486
 38O  N13  N  NR15  0  -0.731  -0.3761  -1.9550  -0.0172
 38O  C15  C  CR16  0  -0.311   2.0843  -2.5495  -0.0087
 38O  C16  C  CR16  0  -0.376   3.3330  -1.9465  -0.0166
 38O  C17  C  CR6   0  -0.394  -2.4510  -0.6071  -0.0291
 38O  C18  C  CR6   0   0.494  -3.0481   0.6666  -0.0335
 38O  C21  C  CR6   0   0.562  -5.2460   1.9568   0.0025
 38O  C23  C  CR16  0  -0.419  -6.6150   2.0020   0.0399
 38O  C24  C  CR16  0  -0.241  -7.3193   0.7999   0.0761
 38O  N2   N  NT    0  -0.412   7.4107   1.0017   0.4071
 38O  N5   N  NT    0  -0.519   4.7698   0.0452  -0.1161
 38O  C9   C  CR16  0  -0.443   2.3605   0.2672  -0.1100
 38O  C10  C  CR56  0   0.220   1.1050  -0.3286  -0.0747
 38O  N11  N  N     0  -0.596  -0.1387   0.2473  -0.0870
 38O  C14  C  CR56  0   0.297   0.9736  -1.7239  -0.0305
 38O  N19  N  NH2   0  -0.866  -2.3016   1.7627  -0.0661
 38O  C20  C  CR66  0  -0.262  -4.5029   0.7650   0.0003
 38O  F22  F  F     0  -0.311  -4.6029   3.1354  -0.0341
 38O  C25  C  CR16  0  -0.332  -6.6530  -0.4021   0.0738
 38O  C26  C  CR66  0   0.396  -5.2549  -0.4218   0.0358
 38O  N27  N  NR16  0  -0.766  -4.6095  -1.6205   0.0348
 38O  C28  C  CR6   0   0.525  -3.2544  -1.8018   0.0055
 38O  H1   H  HCH3  0   0.192   8.6337   2.2141  -0.8526
 38O  H2   H  HCH3  0   0.233   8.8062   2.4764   0.8900
 38O  H3   H  HCH3  0   0.233   9.4835   1.0261   0.1487
 38O  H4   H  HCH2  0   0.239   8.0171  -0.7383  -0.5603
 38O  H5   H  HCH2  0   0.192   7.0727   0.3509  -1.5817
 38O  H6   H  HCH2  0   0.248   5.7496  -1.5706  -0.9963
 38O  H7   H  HCH2  0   0.206   6.0875  -1.3888   0.7274
 38O  H8   H  HCH2  0   0.210   5.0963   0.7584   1.8475
 38O  H9   H  HCH2  0   0.252   4.1783   1.8374   0.8008
 38O  H10  H  HCH2  0   0.192   6.1194   2.4080  -0.5138
 38O  H11  H  HCH2  0   0.239   6.4458   2.6645   1.2047
 38O  H12  H  HNR5  0   0.421  -0.8722  -2.8348   0.0156
 38O  H13  H  HCR6  0   0.261   1.9966  -3.6274   0.0285
 38O  H14  H  HCR6  0   0.266   4.1971  -2.5930   0.0282
 38O  H15  H  HCR6  0   0.289  -7.1250   2.9555   0.0407
 38O  H16  H  HCR6  0   0.283  -8.3999   0.8164   0.1060
 38O  H18  H  HCR6  0   0.255   2.4393   1.3445  -0.1785
 38O  H20  H  HNH2  0   0.412  -2.6976   2.6828  -0.0571
 38O  H21  H  HNH2  0   0.427  -1.2886   1.6449  -0.0850
 38O  H22  H  HCR6  0   0.286  -7.1991  -1.3358   0.1037
 38O  H23  H  HNR6  0   0.418  -5.1694  -2.4616   0.0617
 38O  O29  O  O     0  -0.517  -2.8179  -2.9565   0.0114

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 38O  C4   C3   single    1.517  0.020  1.517
 38O  C4   N5   single    1.448  0.020  1.448
 38O  C3   N2   single    1.447  0.020  1.447
 38O  F22  C21  single    1.343  0.020  1.343
 38O  N2   C1   single    1.445  0.020  1.445
 38O  N2   C7   single    1.447  0.020  1.447
 38O  N5   C6   single    1.457  0.020  1.457
 38O  N5   C8   single    1.404  0.020  1.404
 38O  N19  C18  single    1.327  0.020  1.327
 38O  C6   C7   single    1.515  0.020  1.515
 38O  C9   C8   aromatic  1.397  0.020  1.397
 38O  C9   C10  aromatic  1.390  0.020  1.390
 38O  C8   C16  aromatic  1.413  0.020  1.413
 38O  C21  C23  aromatic  1.370  0.020  1.370
 38O  C21  C20  aromatic  1.405  0.020  1.405
 38O  N11  C10  aromatic  1.371  0.020  1.371
 38O  N11  C12  aromatic  1.324  0.020  1.324
 38O  C10  C14  aromatic  1.402  0.020  1.402
 38O  C23  C24  aromatic  1.394  0.020  1.394
 38O  C18  C20  single    1.459  0.020  1.459
 38O  C18  C17  double    1.407  0.020  1.407
 38O  C16  C15  aromatic  1.387  0.020  1.387
 38O  C20  C26  aromatic  1.405  0.020  1.405
 38O  C12  C17  single    1.452  0.020  1.452
 38O  C12  N13  aromatic  1.358  0.020  1.358
 38O  C14  C15  aromatic  1.384  0.020  1.384
 38O  C14  N13  aromatic  1.369  0.020  1.369
 38O  C17  C28  single    1.440  0.020  1.440
 38O  C24  C25  aromatic  1.374  0.020  1.374
 38O  C26  C25  aromatic  1.399  0.020  1.399
 38O  C26  N27  single    1.361  0.020  1.361
 38O  C28  N27  single    1.367  0.020  1.367
 38O  C28  O29  double    1.234  0.020  1.234
 38O  C1   H1   single    0.970  0.020  1.090
 38O  C1   H2   single    0.970  0.020  1.090
 38O  C1   H3   single    0.970  0.020  1.090
 38O  C3   H4   single    0.970  0.020  1.090
 38O  C3   H5   single    0.970  0.020  1.090
 38O  C4   H6   single    0.970  0.020  1.090
 38O  C4   H7   single    0.970  0.020  1.090
 38O  C6   H8   single    0.970  0.020  1.090
 38O  C6   H9   single    0.970  0.020  1.090
 38O  C7   H10  single    0.970  0.020  1.090
 38O  C7   H11  single    0.970  0.020  1.090
 38O  N13  H12  single    0.860  0.020  1.020
 38O  C15  H13  single    0.930  0.020  1.080
 38O  C16  H14  single    0.930  0.020  1.080
 38O  C23  H15  single    0.930  0.020  1.080
 38O  C24  H16  single    0.930  0.020  1.080
 38O  C9   H18  single    0.930  0.020  1.080
 38O  N19  H20  single    0.860  0.020  1.020
 38O  N19  H21  single    0.860  0.020  1.020
 38O  C25  H22  single    0.930  0.020  1.080
 38O  N27  H23  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 38O  H3   C1   H2   107.87  3.000
 38O  H3   C1   H1   107.74  3.000
 38O  H2   C1   H1   107.72  3.000
 38O  H3   C1   N2   110.16  3.000
 38O  H2   C1   N2   110.00  3.000
 38O  H1   C1   N2   113.18  3.000
 38O  H5   C3   H4   107.06  3.000
 38O  H5   C3   N2   111.63  3.000
 38O  H4   C3   N2   109.26  3.000
 38O  H5   C3   C4   109.20  3.000
 38O  H4   C3   C4   108.41  3.000
 38O  N2   C3   C4   111.14  3.000
 38O  H7   C4   H6   107.31  3.000
 38O  H7   C4   N5   111.95  3.000
 38O  H6   C4   N5   109.54  3.000
 38O  H7   C4   C3   109.12  3.000
 38O  H6   C4   C3   108.04  3.000
 38O  N5   C4   C3   110.74  3.000
 38O  H9   C6   H8   107.20  3.000
 38O  H9   C6   N5   110.26  3.000
 38O  H8   C6   N5   110.78  3.000
 38O  H9   C6   C7   108.16  3.000
 38O  H8   C6   C7   109.45  3.000
 38O  N5   C6   C7   110.88  3.000
 38O  H11  C7   H10  107.19  3.000
 38O  H11  C7   N2   109.30  3.000
 38O  H10  C7   N2   111.66  3.000
 38O  H11  C7   C6   108.56  3.000
 38O  H10  C7   C6   109.22  3.000
 38O  N2   C7   C6   110.80  3.000
 38O  C9   C8   N5   119.53  3.000
 38O  C9   C8   C16  118.91  3.000
 38O  N5   C8   C16  121.54  3.000
 38O  N11  C12  C17  125.23  3.000
 38O  C17  C12  N13  123.33  3.000
 38O  N11  C12  N13  111.44  3.000
 38O  H12  N13  C14  129.13  3.000
 38O  H12  N13  C12  122.97  3.000
 38O  C14  N13  C12  107.90  3.000
 38O  H13  C15  C14  121.98  3.000
 38O  H13  C15  C16  120.42  3.000
 38O  C14  C15  C16  117.59  3.000
 38O  H14  C16  C15  117.38  3.000
 38O  H14  C16  C8   120.20  3.000
 38O  C15  C16  C8   122.42  3.000
 38O  C28  C17  C18  120.96  3.000
 38O  C28  C17  C12  118.20  3.000
 38O  C18  C17  C12  120.84  3.000
 38O  C20  C18  N19  120.41  3.000
 38O  C20  C18  C17  118.97  3.000
 38O  N19  C18  C17  120.62  3.000
 38O  F22  C21  C20  119.42  3.000
 38O  C20  C21  C23  123.82  3.000
 38O  F22  C21  C23  116.75  3.000
 38O  H15  C23  C24  121.48  3.000
 38O  H15  C23  C21  120.02  3.000
 38O  C24  C23  C21  118.50  3.000
 38O  H16  C24  C25  119.87  3.000
 38O  H16  C24  C23  119.51  3.000
 38O  C25  C24  C23  120.62  3.000
 38O  C7   N2   C3   109.65  3.000
 38O  C7   N2   C1   111.73  3.000
 38O  C3   N2   C1   111.82  3.000
 38O  C8   N5   C6   116.40  3.000
 38O  C8   N5   C4   117.73  3.000
 38O  C6   N5   C4   111.43  3.000
 38O  H18  C9   C10  119.60  3.000
 38O  H18  C9   C8   121.39  3.000
 38O  C10  C9   C8   119.01  3.000
 38O  C14  C10  N11  109.47  3.000
 38O  C14  C10  C9   120.79  3.000
 38O  N11  C10  C9   129.73  3.000
 38O  C10  N11  C12  106.08  3.000
 38O  C10  C14  C15  121.26  3.000
 38O  C15  C14  N13  133.64  3.000
 38O  C10  C14  N13  105.10  3.000
 38O  H21  N19  H20  119.93  3.000
 38O  H21  N19  C18  117.64  3.000
 38O  H20  N19  C18  122.42  3.000
 38O  C26  C20  C21  115.68  3.000
 38O  C26  C20  C18  118.51  3.000
 38O  C21  C20  C18  125.80  3.000
 38O  H22  C25  C26  119.54  3.000
 38O  H22  C25  C24  120.66  3.000
 38O  C26  C25  C24  119.80  3.000
 38O  N27  C26  C25  119.10  3.000
 38O  N27  C26  C20  119.33  3.000
 38O  C25  C26  C20  121.58  3.000
 38O  H23  N27  C28  116.05  3.000
 38O  H23  N27  C26  118.04  3.000
 38O  C28  N27  C26  125.91  3.000
 38O  N27  C28  O29  118.31  3.000
 38O  O29  C28  C17  125.37  3.000
 38O  N27  C28  C17  116.32  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 38O  CONST_01  N11  C10  C9   C8    180.00   0.0  0
 38O  CONST_02  C14  C10  C9   C8      0.00   0.0  0
 38O  CONST_03  C14  C15  C16  C8      0.00   0.0  0
 38O  CONST_04  C9   C10  N11  C12   180.00   0.0  0
 38O  CONST_05  C14  C10  N11  C12     0.00   0.0  0
 38O  CONST_06  C10  C14  N13  C12     0.00   0.0  0
 38O  CONST_07  C15  C14  N13  C12   180.00   0.0  0
 38O  CONST_08  C10  N11  C12  N13     0.00   0.0  0
 38O  CONST_09  C9   C10  C14  N13   180.00   0.0  0
 38O  CONST_10  N11  C10  C14  N13     0.00   0.0  0
 38O  CONST_11  C16  C15  C14  N13   180.00   0.0  0
 38O  CONST_12  C9   C8   C16  C15     0.00   0.0  0
 38O  CONST_13  C9   C10  C14  C15     0.00   0.0  0
 38O  CONST_14  N11  C10  C14  C15   180.00   0.0  0
 38O  CONST_15  C10  C9   C8   C16     0.00   0.0  0
 38O  CONST_16  C10  C14  C15  C16     0.00   0.0  0
 38O  CONST_17  C25  C24  C23  C21     0.00   0.0  0
 38O  CONST_18  C25  C26  C20  C21     0.00   0.0  0
 38O  CONST_19  C26  C20  C21  C23     0.00   0.0  0
 38O  CONST_20  C26  C25  C24  C23     0.00   0.0  0
 38O  CONST_21  C20  C21  C23  C24     0.00   0.0  0
 38O  CONST_22  C20  C26  C25  C24     0.00   0.0  0
 38O  CONST_23  C14  N13  C12  N11     0.00   0.0  0
 38O  CONST_24  N5   C8   C16  C15   180.00   0.0  0
 38O  CONST_25  C10  N11  C12  C17   180.00   0.0  0
 38O  CONST_26  C14  N13  C12  C17   180.00   0.0  0
 38O  CONST_27  C10  C9   C8   N5    180.00   0.0  0
 38O  CONST_28  C26  N27  C28  C17     0.00   0.0  0
 38O  CONST_29  F22  C21  C20  C18     0.00   0.0  0
 38O  CONST_30  F22  C21  C23  C24   180.00   0.0  0
 38O  CONST_31  C26  C20  C21  F22   180.00   0.0  0
 38O  CONST_32  C26  N27  C28  O29   180.00   0.0  0
 38O  CONST_33  H13  C15  C16  C8    180.00   0.0  0
 38O  CONST_34  H12  N13  C14  C15     0.00   0.0  0
 38O  CONST_35  H18  C9   C8   C16   180.00   0.0  0
 38O  CONST_36  H16  C24  C23  C21   180.00   0.0  0
 38O  CONST_37  H22  C25  C24  C23   180.00   0.0  0
 38O  CONST_38  H14  C16  C8   N5      0.00   0.0  0
 38O  CONST_39  H15  C23  C21  C20   180.00   0.0  0
 38O  CONST_40  H23  N27  C28  C17   180.00   0.0  0
 38O  Var_01    C6   N5   C4   C3    -54.47  30.0  1
 38O  Var_02    C6   C7   N2   C3     58.49  30.0  1
 38O  Var_03    C7   N2   C3   C4    -58.48  30.0  1
 38O  Var_04    C7   C6   N5   C4     54.76  30.0  1
 38O  Var_05    C9   C8   N5   C4   -174.01  30.0  2
 38O  Var_06    C18  C17  C12  N13   178.58  30.0  2
 38O  Var_07    N5   C4   C3   N2     56.67  30.0  1
 38O  Var_08    N5   C6   C7   N2    -56.84  30.0  1
 38O  Var_09    H1   C1   N2   C3     61.30  30.0  3
 38O  Var_10    H20  N19  C18  C17  -179.12  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 38O  plan-1  C8   0.020
 38O  plan-1  C12  0.020
 38O  plan-1  N13  0.020
 38O  plan-1  C15  0.020
 38O  plan-1  C16  0.020
 38O  plan-1  C17  0.020
 38O  plan-1  N5   0.020
 38O  plan-1  C9   0.020
 38O  plan-1  C10  0.020
 38O  plan-1  N11  0.020
 38O  plan-1  C14  0.020
 38O  plan-1  H12  0.020
 38O  plan-1  H13  0.020
 38O  plan-1  H14  0.020
 38O  plan-1  H18  0.020
 38O  plan-2  C12  0.020
 38O  plan-2  C17  0.020
 38O  plan-2  C18  0.020
 38O  plan-2  C21  0.020
 38O  plan-2  C23  0.020
 38O  plan-2  C24  0.020
 38O  plan-2  N19  0.020
 38O  plan-2  C20  0.020
 38O  plan-2  F22  0.020
 38O  plan-2  C25  0.020
 38O  plan-2  C26  0.020
 38O  plan-2  N27  0.020
 38O  plan-2  C28  0.020
 38O  plan-2  H15  0.020
 38O  plan-2  H16  0.020
 38O  plan-2  H22  0.020
 38O  plan-2  H23  0.020
 38O  plan-2  O29  0.020

